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For example, would Matz-san (for Yukihiro Matsumoto) make sense (at least coming from someone new to Japanese), or would the mixture of the slightly formal "-san" and an informal nickname seem strange?

It does sound strange a little bit for the exact reason you are concerned with, but some people do it anyway. Another source of strangeness is the mixture of a word written in latin alphabet (the sequence 'tz' never appears in Japanese) and the さん which is primarily used for well accomodated words. But perhaps you are going to pronounce it as 'matsu-san' anyway; which is not that bad.
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user458Jul 8 '11 at 13:27

3 Answers
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Of course, it is unlikely that you call Robert "ボビー*様*" (except as joke or if it's part of the nickname), but if you meet a guy and he says "My name is Daisuke, but you can call me Dai!", you'll probably end calling him "ダイ君". And Tomoko will be "トモちゃん". And if you're not that close to the other person, ダイさん and トモさん will be ok too.
Similarly, if you're a red-haired teacher, your friends may call you Ginger先生, and so on…

There really are no hard and fast rules with nicknames plus honorifics when actually speaking. Usually something will end up sticking even though it may be "wrong". For someone new to Japanese, go with -san (for older or business) and -chan (for younger or girlfriends) and then follow the lead of the Japanese people you are with.

For example, one friend of mine is よちゃん. This is what everyone calls him, including younger people and people the same age, he even introduces himself this way in friendly groups. This would be wrong according to the rules, but is what the native Japanese call him.

I've been called ロスちゃん among friends as well as ロスピン, though the ピン is reserved for girlfriend and boyfriend in my experience. In more formal situations, I am generally called ロスさん, even though my last name would be more "correct". When I am the customer, though, it is always last name + さま.

So, really just follow the lead of those around you, this is an area where the rules often give way to whatever feels right.

I confirm that the 'ちゃん' suffix is very common in nicknames of otherwise completely manly man. In fact, in my (limited) experience, it's even more prevalent among some working-class macho Japanese (people doing manual labour etc.) than the rest... The general rule, however, is that the nickname should be one single mora/syllable (よちゃん, あっちゃん etc.), so use with caution.
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Dave♦Jul 9 '11 at 1:27

@Dave - good points here. I don't personally know any construction workers so this is very interesting. To underscore my point that the feeling is more important than the rules, here is some more detail on the よちゃん example: よちゃん happens to be a dentist, so in this case it's really more his 雰囲気 as opposed to social position. My other friend in the same group is also a dentist and NO ONE uses ちゃん with him even those older or technically his superior, I've never even heard his wife use it.
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RossJul 13 '11 at 13:08